75 research outputs found
Poly-Sarcosine and Poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulations
Nanoparticles coated with hydrophilic polymers often show a reduction in
unspecific interactions with the biological environment, which improves their
biocompatibility. The molecular determinants of this reduction are not very
well understood yet, and their knowledge may help improving nanoparticle
design. Here we address, using molecular dynamics simulations, the interactions
of human serum albumin, the most abundant serum protein, with two promising
hydrophilic polymers used for the coating of therapeutic nanoparticles,
poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in
a polymer-water mixture, we show that the two polymers have a very similar
affinity for the protein surface, both in terms of the amount of polymer
adsorbed and also in terms of the type of amino acids mainly involved in the
interactions. We further analyze the kinetics of adsorption and how it affects
the polymer conformations. Minor differences between the polymers are observed
in the thickness of the adsorption layer, that are related to the different
degree of flexibility of the two molecules. In comparison poly-alanine, an
isomer of poly-sarcosine known to self-aggregate and induce protein
aggregation, shows a significantly larger affinity for the protein surface than
PEG and PSar, which we show to be related not to a different patterns of
interactions with the protein surface, but to the different way the polymer
interacts with water
Estimation of protein folding probability from equilibrium simulations
The assumption that similar structures have similar folding probabilities
() leads naturally to a procedure to evaluate for every
snapshot saved along an equilibrium folding-unfolding trajectory of a
structured peptide or protein. The procedure utilizes a structurally
homogeneous clustering and does not require any additional simulation. It can
be used to detect multiple folding pathways as shown for a three-stranded
antiparallel -sheet peptide investigated by implicit solvent molecular
dynamics simulations.Comment: 7 pages, 4 figures, supplemetary material
Molecular Dynamics Simulations of the NGF-TrkA Domain 5 Complex and Comparison with Biological Data
AbstractThe nerve growth factor (NGF) is an important pharmacological target for Alzheimer's and other neurodegenerative diseases. Its action derives partly from its binding to the tyrosine kinase A receptor (TrkA). Here we study energetics and dynamics of the NGF-TrkA complex by carrying out multinanosecond molecular dynamics simulations, accompanied by electrostatic calculations based on the Poisson-Boltzmann equation. Our calculations, which are based on the x-ray structure of the complex, suggest that some of the mutations affecting dramatically the affinity of the complex involve residues that form highly favorable, direct or water-mediated hydrogen bond interactions at the ligand-receptor interface and, in some cases, that also critically participate to the large-scale motions of the complex. Furthermore, our calculations offer a rationale for the small effect on binding affinity observed upon specific mutations involving large changes in electrostatics (i.e., the charged-to-neutral mutations). Finally, these calculations, used along with the mutagenesis data, provide a basis for designing new peptides that mimic NGF in TrkA binding function
Wordom: a program for efficient analysis of molecular dynamics simulations
Summary: Wordom is a versatile program for manipulation of molecular dynamics trajectories and efficient analysis of simulations. Original tools in Wordom include a procedure to evaluate significance of sampling for principal component analysis as well as modules for clustering multiple conformations and evaluation of order parameters for folding and aggregation. The program was developed with special emphasis on user-friendliness, effortless addition of new modules and efficient handling of large sets of trajectories. Availability: The Wordom program is distributed with full source code (in the C language) and documentation for usage and further development as a platform-independent package under a GPL license from http://www.biochem-caflisch.unizh.ch/wordom/ Contact: [email protected]
Folding Pathways of Prion and Doppel
The relevance of various residue positions for the stability and the folding
characteristics of the prion protein are investigated by using molecular
dynamics simulations of models exploiting the topology of the native state.
Highly significant correlations are found between the most relevant sites in
our analysis and the single point mutations known to be associated with the
arousal of the genetic forms of prion disease (caused by the conformational
change from the cellular to the scrapie isoform). Considerable insight into the
conformational change is provided by comparing the folding process of prion and
doppel (a newly discovered protein) sharing very similar native state topology:
the folding pathways of the former can be grouped in two main classes according
to which tertiary structure contacts are formed first enroute to the native
state. For the latter a single class of pathways leads to the native state. Our
results are consistent and supportive of the recent experimental findings that
doppel lacks the scrapie isoform and that such remarkably different behavior
results from differences in the region containing the two strands and
the intervening helix.Comment: 16 pages, 2 tables, 5 figure
High Temperature Unfolding Simulations of the TRPZ1 Peptide
We report high temperature molecular dynamics simulations of the unfolding of the TRPZ1 peptide using an explicit model for the solvent. The system has been simulated for a total of 6 μs with 100-ns minimal continuous stretches of trajectory. The populated states along the simulations are identified by monitoring multiple observables, probing both the structure and the flexibility of the conformations. Several unfolding and refolding transition pathways are sampled and analyzed. The unfolding process of the peptide occurs in two steps because of the accumulation of a metastable on-pathway intermediate state stabilized by two native backbone hydrogen bonds assisted by nonnative hydrophobic interactions between the tryptophan side chains. Analysis of the un/folding kinetics and classical commitment probability calculations on the conformations extracted from the transition pathways show that the rate-limiting step for unfolding is the disruption of the ordered native hydrophobic packing (Trp-zip motif) leading from the native to the intermediate state. But, the speed of the folding process is mainly determined by the transition from the completely unfolded state to the intermediate and specifically by the closure of the hairpin loop driven by formation of two native backbone hydrogen bonds and hydrophobic contacts between tryptophan residues. The temperature dependence of the unfolding time provides an estimate of the unfolding activation enthalpy that is in agreement with experiments. The unfolding time extrapolated to room temperature is in agreement with the experimental data as well, thus providing a further validation to the analysis reported here
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Targeting cavity-creating p53 cancer mutations with small-molecule stabilizers: the Y220X paradigm
We have previously shown that the thermolabile, cavity-creating p53 cancer mutant Y220C can be reactivated by small-molecule stabilizers. In our ongoing efforts to unearth druggable variants of the p53 mutome, we have now analyzed the effects of other cancer-associated mutations at codon 220 on the structure, stability and dynamics of the p53 DNA-binding domain (DBD). We found that the oncogenic Y220H, Y220N and Y220S mutations are also highly destabilizing, suggesting that they are largely unfolded under physiological conditions.
A high-resolution crystal structure of the Y220S mutant DBD revealed a mutation-induced surface crevice similar to that of Y220C, whereas the corresponding pocket’s accessibility to small molecules was blocked in the structure of the Y220H mutant. Accordingly, a series of carbazole-based small molecules, designed for stabilizing the Y220C mutant, also bound to and stabilized the folded state of the Y220S mutant, albeit with varying affinities due to structural differences in the binding pocket of the two mutants. Some of the compounds also bound to and stabilized the Y220N mutant, but not the Y220H mutant. Our data validate the Y220S and Y220N mutant as druggable targets and provide a framework for the design of Y220S or Y220N-specific compounds as well as compounds with dual Y220C/Y220S specificity for use in personalized cancer therap
Fecal microbiota transplantation to improve efficacy of immune checkpoint inhibitors in renal cell carcinoma (TACITO trial)
Background:
Renal cell carcinoma (RCC) is the 6° most common cancer in men and the 8° in women in the USA. In Italy RCC incidence was 11,500 new cases in 2017, while mortality was 3,371 cases in 2015. Increasing evidence suggests that response to immune checkpoint inhibitors (ICIs), a novel treatment for advanced RCC (aRCC) and other epithelial tumors, can be influenced by the patient gut microbiota. Fecal microbiota transplantation (FMT) is a novel treatment option aimed to restore healthy gut microbiota, and is the most effective therapy for recurrent C. difficile infection. Preliminary nonrandomized findings show that FMT is able to improve efficacy of ICIs in patients with advanced melanoma. The aim of this study is to evaluate, through a double-blinded placebo-controlled randomized clinical trial, the efficacy of targeted FMT (from donors who are responding to ICIs) in improving response rates to ICIs in subjects with aRCC.
Methods:
50 patients who are about to receive, or have started by <8 weeks, pembrolizumab + axitinib as first-line therapy for aRCC will be enrolled. Exclusion criteria include major comorbidities, concomitant GI or autoimmune disorders, or HIV, HBV, HCV infection, continuative corticosteroid therapy, previous treatment with systemic immune-suppressants or immune-modulatory drugs, antibiotic therapy within 4 weeks prior to enrollment. Stool samples and clinical data will be collected at baseline. Then, patients will be randomized to donor FMT or placebo FMT. They will receive the first infusion by colonoscopy and then oral frozen fecal or placebo capsules (8 capsules t.i.d.) 90 and 180 days after the first FMT. Stool donors will be searched among long-term (>12 months) responders to ICIs, and will be selected by following protocols recommended by international guidelines. Patients in the FMT group will always receive feces from the same donor throughout the three fecal transplants. Frozen fecal batches and frozen fecal capsules will be manufactured according to international guidelines. Patients will be followed-up 7, 15, 30, 90, 180, 270, and 360 days after randomization for clinical evaluation and collection of stool samples. Patients will also undergo radiological assessment at 90, 180, 270 and 360 days after randomization. Microbiome analysis will be performed with shotgun metagenomics. The primary endpoint is the progression-free survival (PFS) at 12 months. Secondary endpoints are: objective response rate at 12 months; overall survival at 12 months; adverse events after FMT; microbiome changes after FMT. Sample size calculation was based on the hypothesis that FMT can improve the 1-year PFS rate from 60% (reported 1-year PFS for SOC) to 80% wen associated to SOC. Clinical trial information: NCT04758507
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